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## Hierarchy For All Packages

Package Hierarchies:
  org.metaqtl, org.metaqtl.adapter, org.metaqtl.algo, org.metaqtl.bio, org.metaqtl.bio.entity, org.metaqtl.bio.entity.adapter, org.metaqtl.bio.entity.bean, org.metaqtl.bio.entity.factory, org.metaqtl.bio.util, org.metaqtl.factory, org.metaqtl.graph, org.metaqtl.main, org.metaqtl.numrec, org.metaqtl.util

## Class Hierarchy

- java.lang.Object
  - java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    - java.util.AbstractList<E> (implements java.util.List<E>)
      - java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        - org.metaqtl.bio.entity.BioEntityCollection (implements java.util.Collection<E>, org.metaqtl.bio.IBioEntity)
  - org.metaqtl.graph.AnchoredElement
    - org.metaqtl.graph.Layer
      - org.metaqtl.graph.ChromLayer
      - org.metaqtl.graph.QtlLayer
      - org.metaqtl.graph.QtlPartitionLayer
      - org.metaqtl.graph.QtlTreeLayer
  - org.metaqtl.bio.util.BioCrossTypes
  - org.metaqtl.bio.entity.BioEntity (implements org.metaqtl.bio.IBioEntity)
    - org.metaqtl.bio.entity.BioEntityContainer (implements org.metaqtl.bio.IBioEntity)
      - org.metaqtl.bio.entity.AlleleContainer (implements org.metaqtl.bio.IBioLocus)
        - org.metaqtl.bio.entity.Locus (implements org.metaqtl.bio.IBioLocus)
          - org.metaqtl.bio.entity.Marker (implements org.metaqtl.bio.IBioLocus)
          - org.metaqtl.bio.entity.QTL (implements org.metaqtl.bio.IBioLocus)
      - org.metaqtl.bio.entity.GroupContainer (implements org.metaqtl.bio.IBioGenome)
        - org.metaqtl.bio.entity.GeneticMap
      - org.metaqtl.bio.entity.Individual
      - org.metaqtl.bio.entity.IndividualContainer (implements org.metaqtl.bio.IBioPopulation)
        - org.metaqtl.bio.entity.Population (implements org.metaqtl.bio.IBioPopulation)
          - org.metaqtl.bio.entity.CrossPopulation (implements org.metaqtl.bio.IBioCross)
      - org.metaqtl.bio.entity.LocusContainer (implements org.metaqtl.bio.IBioLGroup)
        - org.metaqtl.bio.entity.LGroup (implements org.metaqtl.bio.IBioLGroup)
    - org.metaqtl.bio.entity.Ontology (implements org.metaqtl.bio.IBioOntology)
    - org.metaqtl.bio.entity.OntologyTerm (implements org.metaqtl.bio.IBioOntologyTerm)
  - org.metaqtl.bio.entity.adapter.BioEntityAdapter (implements org.metaqtl.bio.IBioAdapter)
    - org.metaqtl.bio.entity.adapter.BioEntityCollectionAdapter (implements org.metaqtl.bio.IBioAdapter)
    - org.metaqtl.bio.entity.adapter.GeneticMapBeanAdapter (implements org.metaqtl.bio.IBioAdapter)
    - org.metaqtl.bio.entity.adapter.LGroupBeanAdapter (implements org.metaqtl.bio.IBioAdapter)
    - org.metaqtl.bio.entity.adapter.LocusBeanAdapter
    - org.metaqtl.bio.entity.adapter.OntologyBeanAdapter
    - org.metaqtl.bio.entity.adapter.OntologyTermBeanAdapter
  - org.metaqtl.bio.entity.bean.BioEntityBean
    - org.metaqtl.bio.entity.bean.BioEntityCollectionBean
    - org.metaqtl.bio.entity.bean.GeneticMapBean
    - org.metaqtl.bio.entity.bean.LGroupBean
    - org.metaqtl.bio.entity.bean.LocusBean
    - org.metaqtl.bio.entity.bean.OntologyBean
    - org.metaqtl.bio.entity.bean.OntologyTermBean
  - org.metaqtl.bio.entity.factory.BioEntityFactory
    - org.metaqtl.bio.entity.factory.MapChartFactory
    - org.metaqtl.bio.entity.factory.MapMakerFactory
    - org.metaqtl.bio.entity.factory.MapRawFactory
    - org.metaqtl.bio.entity.factory.MapTabFactory
    - org.metaqtl.bio.entity.factory.OntologyTabFactory
    - org.metaqtl.bio.entity.factory.XmlBioEntityFactory
      - org.metaqtl.bio.entity.factory.XmlBioEntitiesFactory
      - org.metaqtl.bio.entity.factory.XmlGeneticMapFactory
      - org.metaqtl.bio.entity.factory.XmlOntologyFactory
  - org.metaqtl.bio.util.BioEntityNameComparator (implements java.util.Comparator<T>)
  - org.metaqtl.bio.util.BioLocusTypes
  - org.metaqtl.bio.util.BioUtilities
  - org.metaqtl.graph.ChromAxe
  - org.metaqtl.ChromCluster
  - org.metaqtl.ChromCluster.ClusterEdge
  - org.metaqtl.ChromCluster.ClusterGraph
  - org.metaqtl.graph.ChromGraph
  - org.metaqtl.graph.ChromLayer.CMrkTickPath
  - org.metaqtl.graph.ChromLayer.CMrkTickPoint
  - org.metaqtl.Chromosome
  - org.metaqtl.adapter.ChromosomeAdapter
  - org.metaqtl.CMarkerSequence
  - org.metaqtl.main.CmdLineParser
  - org.metaqtl.main.CmdLineParser.Option
    - org.metaqtl.main.CmdLineParser.Option.BooleanOption
    - org.metaqtl.main.CmdLineParser.Option.DoubleOption
    - org.metaqtl.main.CmdLineParser.Option.IntegerOption
    - org.metaqtl.main.CmdLineParser.Option.LongOption
    - org.metaqtl.main.CmdLineParser.Option.StringOption
  - org.metaqtl.algo.CMSAlgorithm
  - org.metaqtl.factory.DubiousLocusFactory
  - org.metaqtl.algo.EMAlgorithm
  - org.metaqtl.EMCriteria (implements java.io.Serializable)
  - org.metaqtl.EMResult
  - org.metaqtl.factory.EMResultFactory
  - org.metaqtl.util.GeneticMapProperties
  - org.metaqtl.graph.GraphFactory
  - org.metaqtl.graph.GraphShape
    - org.metaqtl.graph.ChromShape
    - org.metaqtl.graph.QtlShape
  - org.metaqtl.algo.HClustAlgorithm
  - org.metaqtl.bio.util.LGroupPosition (implements org.metaqtl.bio.util.ILGroupPosition)
    - org.metaqtl.bio.util.EstimatedLocusPosition
    - org.metaqtl.bio.util.StaticLocusPosition
  - org.metaqtl.bio.util.LocusPositionComparator (implements java.util.Comparator<T>)
  - org.metaqtl.util.LocusProperties
  - org.metaqtl.MapCluster
  - org.metaqtl.factory.MapDBFactory
  - org.metaqtl.util.MappingFunction
  - org.metaqtl.algo.MetaAlgorithm (implements org.metaqtl.IMetaAlgorithm)
    - org.metaqtl.algo.ClustAlgorithm
      - org.metaqtl.algo.QtlClustAlgorithm
      - org.metaqtl.algo.QtlTreeAlgorithm
    - org.metaqtl.algo.MetaMapAlgorithm
    - org.metaqtl.algo.QtlProjAlgorithm
  - org.metaqtl.MetaChrom
  - org.metaqtl.MetaDico
  - org.metaqtl.factory.MetaDicoFactory
  - org.metaqtl.graph.MetaGraph
  - org.metaqtl.graph.MetaGraphPar
  - org.metaqtl.factory.MetaGraphParFactory
  - org.metaqtl.main.MetaMain
    - org.metaqtl.main.A2Xml
    - org.metaqtl.main.ConsMap
    - org.metaqtl.main.InfoMap
    - org.metaqtl.main.MapView
    - org.metaqtl.main.MetaDB
    - org.metaqtl.main.MMapView
    - org.metaqtl.main.MQTLView
    - org.metaqtl.main.QTLClust
    - org.metaqtl.main.QTLClustInfo
    - org.metaqtl.main.QTLModel
    - org.metaqtl.main.QTLProj
    - org.metaqtl.main.QTLTree
    - org.metaqtl.main.Xml2A
  - org.metaqtl.MetaMap
  - org.metaqtl.adapter.MetaMapAdapter
  - org.metaqtl.factory.MetaMapSummaryFactory
  - org.metaqtl.MetaQtlAnalysis
  - org.metaqtl.adapter.MetaQtlAnalysisAdapter
  - org.metaqtl.factory.MetaQtlAnalysisFactory
  - org.metaqtl.factory.MetaQtlAnalysisModelFactory
  - org.metaqtl.factory.MetaQtlAnalysisSummaryFactory
  - org.metaqtl.MetaQtlData
  - org.metaqtl.MetaQtlModel
  - org.metaqtl.factory.MetaQtlModelFactory
  - org.metaqtl.MetaQtlResult
  - org.metaqtl.MultiFitResult
  - org.metaqtl.bio.util.NumberFormat
  - org.metaqtl.numrec.NumericalUtilities
  - org.metaqtl.util.OffspringManager
  - org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
  - org.metaqtl.graph.PaletteColor
  - org.metaqtl.bio.entity.bean.PropertyBean
  - org.metaqtl.Qtl
  - org.metaqtl.Qtl.QTLCross (implements java.io.Serializable)
  - org.metaqtl.Qtl.QTLProj (implements java.io.Serializable)
  - org.metaqtl.Qtl.QTLStats (implements java.io.Serializable)
  - org.metaqtl.Qtl.QTLSupport (implements java.io.Serializable)
  - org.metaqtl.Qtl.QTLTrait (implements java.io.Serializable)
  - org.metaqtl.adapter.QtlAdapter
  - org.metaqtl.graph.QtlLayerBuffer
  - org.metaqtl.QtlPartition
  - org.metaqtl.adapter.QtlPartitionAdapter
  - org.metaqtl.graph.QtlUnit
  - org.metaqtl.algo.SVDAlgorithm
  - org.metaqtl.bio.util.TabulatedReader
  - org.metaqtl.bio.util.TabulatedWriter
  - java.lang.Throwable (implements java.io.Serializable)
    - java.lang.Exception
      - org.metaqtl.main.CmdLineParser.OptionException
        - org.metaqtl.main.CmdLineParser.IllegalOptionValueException
        - org.metaqtl.main.CmdLineParser.UnknownOptionException
          - org.metaqtl.main.CmdLineParser.NotFlagException
          - org.metaqtl.main.CmdLineParser.UnknownSuboptionException
  - org.metaqtl.Tree
  - org.metaqtl.factory.TreeFactory
  - org.metaqtl.TreeNode (implements java.io.Serializable)

## Interface Hierarchy

- org.metaqtl.bio.IBioAdaptable
  - org.metaqtl.bio.IBioAllele
  - org.metaqtl.bio.IBioCross
  - org.metaqtl.bio.IBioEntity
    - org.metaqtl.bio.IBioAllele
    - org.metaqtl.bio.IBioCross
    - org.metaqtl.bio.IBioGenome
    - org.metaqtl.bio.IBioIndividual
    - org.metaqtl.bio.IBioLGroup
    - org.metaqtl.bio.IBioLocus
    - org.metaqtl.bio.IBioOntology
    - org.metaqtl.bio.IBioOntologyTerm
    - org.metaqtl.bio.IBioPopulation
      - org.metaqtl.bio.IBioCross
  - org.metaqtl.bio.IBioGenome
  - org.metaqtl.bio.IBioIndividual
  - org.metaqtl.bio.IBioLGroup
  - org.metaqtl.bio.IBioLocus
  - org.metaqtl.bio.IBioOntology
  - org.metaqtl.bio.IBioOntologyTerm
  - org.metaqtl.bio.IBioPopulation
    - org.metaqtl.bio.IBioCross
- org.metaqtl.bio.IBioAdapter
- org.metaqtl.bio.entity.IBioConstants
- org.metaqtl.bio.IBioCrossTypes
- org.metaqtl.bio.IBioEntityTypes
- org.metaqtl.IBioGenomeProperties
- org.metaqtl.bio.IBioIndividualTree
- org.metaqtl.IBioLGroupProperties
- org.metaqtl.IBioLocusProperties
- org.metaqtl.bio.entity.IGeneticMapProperties
- org.metaqtl.bio.util.ILGroupPosition
- org.metaqtl.IMetaAlgorithm
- org.metaqtl.IMetaQtlConstants
- org.metaqtl.bio.IOntologyTermProperties
- org.metaqtl.numrec.NumericalUtilities.Function
- org.metaqtl.numrec.NumericalUtilities.NRFunction

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